Gendo is out to do some good, in the only way that he can; by being the most magnificent, manipulative bastard that he can be. Rei is out to help us all, by doing SCIENCE! Please Read & Review! Note: Chapter 32 has been updated with a timeline and notes down at the bottom. Thank you for reading and sharing your feedback.

DISCLAIMER: I do not own Evangelion; it is owned by Anno and Gainax. If they want me to remove this, I will.

This is my first fanfic. It's going off a few assumptions:Gendo Ikari is a good man.Good is not always nice.Just because something is personal, does not mean that is important in the grand scheme of things.

So, just because Gendo loves his son does not stop him from manipulating his entire life in order to accomplish the Work. If he is to stop terrible things from happening, he has to make sacrifices. So, another alternate character interpretation piece. That aside, I'm going to try to keep the completely OOC to a minimum, but I make no promises.

Please read and review, I'm trying to work on my writing skills!

"A character is talking"

A character is thinking

Matters of Faith

The problem with Shinji, his son, was that he sometimes needed a push in the right direction. Gendo Ikari stared impassively down at his son, standing below him down in the Evangelion cages, in between Dr. Akagi and Captain Katsuragi. Shinji Ikari was a good person, but easily hurt because of his sensitive nature. The fact that he had caused no shortage of emotional trauma to his son did not escape him; but there was nothing to do for it. Had he kept the boy close with him, he would still have been alone as Gendo put his entirety into the Work. Better that he be sent to caretakers elsewhere, hidden away from the horror of the Work and the political intrigues and power plays of SEELE. Although he had not seen his son in many years, Gendo knew that his son was a good boy, if only because he was a good man.

Unfortunately, good is not always nice, and just because something was personal did not make it important.

Gendo stared down at his son, who looked away, muttering about how it was impossible for him to pilot something of this magnitude without ever having been trained for it. Gendo knew that Shinji wanted to help, but he was convinced that he couldn't. What he needed was a push in the right direction. Something on a smaller scale to focus on, instead of the enormity of the fate of mankind. Fortunately enough, Gendo had just the thing to focus Shinji.

He turned to a side panel and opened a link to the bridge. The Sub-Commander appeared on one of the screens. "Fuyutsuki, wake up Rei. The spare is useless."

The aging professor looked shocked at this statement, which completely contradicted the conversation he and his ex protege had had earlier in the day.

"Can we use her?" His voice was uncertain and matched his look of dismay.

"She's not dead yet." Gendo waited as Fuyutsuki paged Rei's room, keeping his eyes on the down-turned face of his son, who was clenching his fists, and most likely grinding his teeth. He suppressed a momentary urge to grin. Rei's tired, quite voice came over the channel, the words Sound Only displaying on the vid screen.

"Rei, the spare is useless. You will do it again." Gendo keep his voice even and detached, only half listening to the girl's whispered acceptance of what would most likely be her death sentence. He watched Shinji shaking on the catwalk as the doctor called for the Evangelion Unit 01 to be prepped for Rei.

When Shinji's look of utter shock and outrage appeared on his face as he first saw the badly injured girl being wheeled out towards the plug, Gendo could not contain his grin, even as the base shook under the Angel's assault. The grin threated to give way to joyous laughter as he watched his son cradle the girl in his arms, staring down at her. He now had his focus. Again the entire Geo-front shook, and as a large girder beam fell towards the children, Unit 01's arm broke loose, smashing the beam away from them.

Shinji looked up at his father, who was staring down at him as he held the fragile blue haired girl in his arms, feeling the pounding of her heart along with his own, as her blood soaked into his shirt and pants. "I'll do it!" he cried out- "I'll pilot it." The doctors came to take the girl Rei from his arms, and when he looked again to his father, he saw only the man's back as he left the observation bay.

----

As the bridge staff hurried to complete the final preparations to synchronize Shinji with the Evangelion, Gendo watched the proceedings from his throne above, keeping an eye on the monitor showing Shinji's face. Fuyutsuki stood next to him, hands clasped behind his back.

"You never actually intended to have Rei pilot the Evangelion, did you? This was just another one of your gambits, maneuvering your pieces around on the chessboard." The older man's voice was low and lost in the general hubbub of the bridge, and only Gendo could hear him. "

What would you have done if he still refused? We're not even sure if Rei can synch up with Unit 01." His tone was accusatory, but not harsh.

"It is inconceivable that Shinji would still refuse to pilot after seeing the condition Rei is in. Every fiber of his being would cry out against such a thing; and I am sure that the thought of still not piloting it after that never even crossed his mind. It would be an Alien concept, to do such a thing so horrific." Commander Ikari's voice was calm and even, as if he was bored with the whole conversation.

"What of the pause then? Before he called out, he just sat there, looking at Rei. Couldn't he have been weighing his life against hers then?"

"You do my son a grave injustice and discredit. He was merely in a state of shock at the extent of her injuries, and the apparent fact that I, his father, a man who has summoned him here was going to send a girl out to certain death. He knew that as son as saw her on the gurney that he was going to pilot in her stead."

The two men gave their attention the the purple haired captain below them; she was asking if they wanted to cancel the deployment on the Evangelion.

"No. We must defeat the Angel. That is all that matters."

She turned back to the front of the bridge, and sang out the command that marked the changing of the world.

"Eva Launch!" she cried, and thus Shinji was sent forth to do battle with the Angel, for Rei, and for all mankind.

Gendo grinned underneath his gloves.

----

As they stared at the silent Evangelion spewing blood and coolant from the injured head, leaning up against a shattered building, it's ruined arm lying atop another building, Fuyutsuki frowned as the bridge crew frantically attempted to achieve contact with the Evangelion and it's Pilot. He glanced down at Gendo, who stared impassively as ever at the main screens, not even sweating. How can he be so calm? This is a disaster! Lieutenant Ibuki cried out in disbelief as Unit 01 reactivated itself, and a bestial roar filled the speakers. The bezerkergang was upon Shinji. As the bio-mechanical titan raged across the screen, slamming into the Angel, it's cries of anger drowned out the shouts of the crew below that this was impossible.

Fuyutsuki had only one thing to say on the matter. "We've won."

Gendo grinned like a madman underneath the cover of his gloves. If anyone had looked up at him they would have only seen him sitting impassively there, the light reflecting from off his old sunglasses hiding the fact that joy and triumph danced in his eyes.

"Yes, Fuyutsuki, we have won. It is only a matter of time now. Nothing can stop what has begun today, As long as we have Unit 01, the Third Child, and Rei, everything else is a matter of patient waiting. We have won the long war, and no one will stand in my way" He paused as the Angel, which undoubtedly would have been shitting itself in sheer, unmitigated terror had it the biological means to do so, wrap itself around the Evangelion in a last ditch effort to take it's killer with it. Light flashed across the screen as the crucifix of light stabbed into the sky and blood began to rain down. Gendo stood up from his seat and turned towards the elevator.

"Ensure that Section 2 maintains watch on him. Minor intrusion into his life only, but if anything begins to get out of hand, they are to fall with all the fury of heaven's hosts." He paused for a moment, glancing back at the screen. "The real ones, that is."

Fuyutsuki smirked at the Commander's back as he entered the lift and ascended higher into the vast building that made up the headquarters of NERV. You have completely upset your son's life, all according to your script for him, and you want him to have some semblance of normalcy in his life until the very end. You have molded his mind and psyche into a fragile, sensitive introvert, isolated from all. You have done this a thousand times more to Rei. And yet, you love them both dearly. But still, you will sacrifice everything to accomplish your goals.

Fuyutsuki snorted, sitting down at the desk, calling up the orders for Section 2.

If only I could see the world in black and white like you do. It would make this job a lot easier.

The author would like to thank you for your continued support. Your review has been posted.